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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/resfinder">Debian Med / resfinder</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/resfinder/commit/86815e3ed1672c6d4b8b77e8b68793f5b2207b74">86815e3e</a></strong>
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<span>by Andreas Tille</span>
<i>at 2018-06-25T13:47:02+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.3.0</pre>
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<h4>1 changed file:</h4>
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<li class="file-stats">
<a href="#f528b86ea4fbbf9b164847c09565a05eea2513cc">
resfinder.pl
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<h4>Changes:</h4>
<li id="f528b86ea4fbbf9b164847c09565a05eea2513cc">
<a href="https://salsa.debian.org/med-team/resfinder/commit/86815e3ed1672c6d4b8b77e8b68793f5b2207b74#f528b86ea4fbbf9b164847c09565a05eea2513cc"><strong>resfinder.pl</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,7 +10,7 @@ use Try::Tiny::Retry;</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">constant</span> <span class="nv" style="color: teal;">PROGRAM_NAME</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'ResFinder_v2.pl'</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">constant</span> <span class="nv" style="color: teal;">PROGRAM_NAME_LONG</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'Findes antimicrobial resitance genes for a sequence or genome'</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">constant</span> <span class="nv" style="color: teal;">VERSION</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'2.<span class="idiff left right">1</span>'</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">constant</span> <span class="nv" style="color: teal;">VERSION</span> <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'2.<span class="idiff left right">3</span>'</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="perl"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#Global variables</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$BLAST</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="465" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -465,7 +465,7 @@ foreach my $element(@Antimicrobial){</td>
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<pre style="margin: 0;"> <span id="LC465" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$Seqs_genome_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">grep_ids</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">seqs</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: teal;">$Seqs_input</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">ids</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">@array_for_getting_genome_seq</span><span class="p">);</span> </span>
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<pre style="margin: 0;"> <span id="LC466" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="nv" style="color: teal;">@</span><span class="p">{</span> <span class="nv" style="color: teal;">$Seqs_genome_ref</span> <span class="p">})</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$contig</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">lc</span><span class="p">(</span><span class="nv" style="color: teal;">$_</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">seq</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$length_contig</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: teal;">$contig</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">#Redundant, da jeg ogs<span class="idiff left right"></span> v.h.a. bioperl finder hit length</span></span>
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$length_contig</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: teal;">$contig</span><span class="p">);</span> <span class="c1" style="color: #998; font-style: italic;">#Redundant, da jeg ogs<span class="idiff left right">� v</span>.h.a. bioperl finder hit length</span></span>
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="perl"> </span>
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># Getting the right sub_contig depends on which strand the hit is on</span></span>
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<pre style="margin: 0;"> <span id="LC471" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># If the hit is on the +1 </span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="490" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -490,7 +490,7 @@ foreach my $element(@Antimicrobial){</td>
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<pre style="margin: 0;"> <span id="LC490" class="line" lang="perl"> <span class="nv" style="color: teal;">$variant</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC491" class="line" lang="perl"> <span class="nv" style="color: teal;">$major_variants_detector</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC492" class="line" lang="perl"> <span class="nv" style="color: teal;">$sub_contig</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: teal;">$contig</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="p">(</span> <span class="nv" style="color: teal;">$HIT_START</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">}</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">((</span><span class="nv" style="color: teal;">$QUERY_LENGTH</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">}</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: teal;">$no_gaps_gene</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$QUERY_START</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">})));</span></span>
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#If, as here, the HSP only starts some nucleotides within the mlst allele, a number of spaces must be written before the matching string from the genome. Likewise, the match-string (the "||<span class="idiff left right">Ê|||Ê</span>||") should be preceeded by spaces</span></span>
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#If, as here, the HSP only starts some nucleotides within the mlst allele, a number of spaces must be written before the matching string from the genome. Likewise, the match-string (the "||<span class="idiff left right">�|||�||")</span> should be preceeded by spaces</span></span>
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="perl"> <span class="nv" style="color: teal;">$spaces_hit</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$QUERY_START</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">}</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$HIT_START</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">}</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="perl"> <span class="nv" style="color: teal;">$spaces_match_string</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$QUERY_START</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC496" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span> </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -705,7 +705,7 @@ foreach my $element(@Antimicrobial){</td>
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<pre style="margin: 0;"> <span id="LC705" class="line" lang="perl"> <span class="nv" style="color: teal;">$variant</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC706" class="line" lang="perl"> <span class="nv" style="color: teal;">$major_variants_detector</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC707" class="line" lang="perl"> <span class="nv" style="color: teal;">$sub_contig</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: teal;">$contig</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="p">(</span> <span class="nv" style="color: teal;">$HIT_START</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">}</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">((</span><span class="nv" style="color: teal;">$QUERY_LENGTH</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">}</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: teal;">$no_gaps_gene</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$QUERY_START</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">})));</span></span>
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<pre style="margin: 0;">-<span id="LC708" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># If, as here, the HSP only starts some nucleotides within the mlst allele, a number of spaces must be written before the matching string from the genome. Likewise, the match-string (the "||<span class="idiff left right">Ê|||Ê</span>||") should be preceeded by spaces</span></span>
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># If, as here, the HSP only starts some nucleotides within the mlst allele, a number of spaces must be written before the matching string from the genome. Likewise, the match-string (the "||<span class="idiff left right">�|||�||")</span> should be preceeded by spaces</span></span>
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="perl"> <span class="nv" style="color: teal;">$spaces_hit</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$QUERY_START</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">}</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$HIT_START</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">}</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="perl"> <span class="nv" style="color: teal;">$spaces_match_string</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$QUERY_START</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="perl"> <span class="p">}</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -860,7 +860,7 @@ foreach my $element(@Antimicrobial){</td>
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860
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<pre style="margin: 0;"> <span id="LC860" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#print $ABres_substr . "\n";</span></span>
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861
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<pre style="margin: 0;"> <span id="LC861" class="line" lang="perl"> <span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: teal;">@</span><span class="p">{</span><span class="nv" style="color: teal;">$GENE_ALIGN_QUERY_HASH</span><span class="p">{</span><span class="nv" style="color: teal;">$gene</span><span class="p">}},</span> <span class="nv" style="color: teal;">$ABres_substr</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC862" class="line" lang="perl"> </span>
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<pre style="margin: 0;">-<span id="LC863" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#Printing spaces before the match string with the "||<span class="idiff left right">Ê||||Ê||Ê</span>||" and the string itself</span></span>
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<pre style="margin: 0;">+<span id="LC863" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#Printing spaces before the match string with the "||<span class="idiff left right">�||||�||�||" an</span>d the string itself</span></span>
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864
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<pre style="margin: 0;"> <span id="LC864" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#print " ";</span></span>
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865
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865
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<pre style="margin: 0;"> <span id="LC865" class="line" lang="perl"> <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$string_spaces</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">#For saving the spaces as a string of spaces instead of a number of spaces</span></span>
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866
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866
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<pre style="margin: 0;"> <span id="LC866" class="line" lang="perl"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="p">;</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: teal;">$spaces_match_string</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="nv" style="color: teal;">$i</span><span class="p">){</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -969,7 +969,7 @@ foreach my $key (sort keys %GENE_RESULTS_HASH2) {</td>
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<pre style="margin: 0;"> <span id="LC969" class="line" lang="perl"> <span class="nv" style="color: teal;">$outStr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$outStr</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">": WARNING2, "</span><span class="p">;</span> </span>
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<pre style="margin: 0;"> <span id="LC970" class="line" lang="perl"> <span class="p">}</span> </span>
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971
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971
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<pre style="margin: 0;"> <span id="LC971" class="line" lang="perl"> <span class="nv" style="color: teal;">$alignment</span> <span class="o" style="font-weight: 600;">.=</span> <span class="nv" style="color: teal;">$outStr</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"ID: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"%, HSP/Length: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">", Contig name: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">", Position: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n\n"</span><span class="p">;</span></span>
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972
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<pre style="margin: 0;">-<span id="LC972" class="line" lang="perl"> <span class="nv" style="color: teal;">$hits_in_seq</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$outStr</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"ID: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"%, HSP/Length: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">", Positions in reference: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$qStart</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">".."</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$qEnd</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">", Contig name: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">", Position: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n"</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">#m<span class="idiff left right"></span>ske forkert text</span></span>
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972
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<pre style="margin: 0;">+<span id="LC972" class="line" lang="perl"> <span class="nv" style="color: teal;">$hits_in_seq</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$outStr</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"ID: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"%, HSP/Length: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">", Positions in reference: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$qStart</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">".."</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$qEnd</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">", Contig name: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">", Position: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n"</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">#m<span class="idiff left right">�sk</span>e forkert text</span></span>
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973
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973
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<pre style="margin: 0;"> <span id="LC973" class="line" lang="perl"> <span class="nv" style="color: teal;">$resalign</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n"</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="974" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
974
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974
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<pre style="margin: 0;"> <span id="LC974" class="line" lang="perl"> </span>
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975
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975
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<pre style="margin: 0;"> <span id="LC975" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;"># now print the alleles</span></span>
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